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The "Unable to read from standard input" message is still with us; the reports we're getting from versions including the diagnostics added while investigating win-plink-stdin-eof say "The handle is invalid".
All reports so far occur when Plink is run by some other program, and cannot be reproduced when the same command is run from the Windows command-line or Cygwin.
Reports:
This blog posting suggests an understanding of the problem with Cygwin rsync at least.